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Yorodumi- PDB-5ecu: The unliganded structure of Caldicellulosiruptor saccharolyticus GH5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ecu | ||||||
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Title | The unliganded structure of Caldicellulosiruptor saccharolyticus GH5 | ||||||
Components | Cellulase | ||||||
Keywords | HYDROLASE / Caldicellulosiruptor / GH5 / TIM-barrel | ||||||
Function / homology | Function and homology information cellulase / cellulase activity / cellulose catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Caldicellulosiruptor saccharolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Alahuhta, P.M. / Lunin, V.V. | ||||||
Citation | Journal: To Be Published Title: The structure of Caldicellulosiruptor saccharolyticus GH5 Authors: Alahuhta, P.M. / Lunin, V.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ecu.cif.gz | 188 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ecu.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ecu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/5ecu ftp://data.pdbj.org/pub/pdb/validation_reports/ec/5ecu | HTTPS FTP |
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-Related structure data
Related structure data | 1g01S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 62571.398 Da / Num. of mol.: 1 / Fragment: UNP residues 30-576 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldicellulosiruptor saccharolyticus (bacteria) Gene: Csac_0678 / Production host: Escherichia coli (E. coli) / References: UniProt: A4XHB2, cellulase |
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-Non-polymers , 6 types, 436 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.0 M sodium malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 83455 / % possible obs: 100 % / Redundancy: 59 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 42.5 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 40 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G01 Resolution: 1.5→19.96 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.197 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.801 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→19.96 Å
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